Research workbench
SARS-cov-2 spike in complex with IgG 553-60 (2-up trimer)
Analyse SARS-cov-2 spike in complex with IgG 553-60 (2-up trimer) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WOB
- Type
- protein
- Length
- 4,476 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; MAB60 vh; MAB60 vl
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Spike glycoprotein | protein | 1076 | 18% helix, 28% strand | P0DTC2 |
| D, F, H | MAB60 vh | protein | 204 | 2% helix, 34% strand | — |
| B, G, I | MAB60 vl | protein | 212 | 1% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains A, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.82 | 0.86 | 95 | empty |
| 2 | 856 | 0.82 | 0.84 | 86 | empty |
| 3 | 828 | 0.81 | 0.84 | 69 | empty |
| 4 | 834 | 0.80 | 0.83 | 73 | empty |
| 5 | 577 | 0.78 | 0.84 | 49 | empty |
Interfaces
14 interfaces between chains.
- A–C · 4692 Ų buried · 47 hydrogen bonds · protein-protein
- A–E · 4339 Ų buried · 33 hydrogen bonds · protein-protein
- C–E · 4179 Ų buried · 30 hydrogen bonds · protein-protein
- D–B · 1807 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 1735 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 38 glycan (disulfide, N-glycosylation).
Compared structures
- 7WOB · SARS-CoV-2 Spike in complex with IgG 553-60 (2-up trimer) · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7WOB · PDBe 7WOB · UniProt P0DTC2
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